Last week's decision by members of the FDA union to accept the government's deal on pensions may have looked as though the union's members – the most senior civil servants in Whitehall – are now happy with the arrangements.

In fact, although the vote (almost three to one in favour on a turnout of 43%) may look like an endorsement of the scheme, it is nothing of the sort. There are many aspects of the changes that members remain extremely unhappy with, and it will be difficult for members to draw a line under the issue of pension reform when they have just faced increases of up to 2.3% to pension contributions this year, with further increases planned for 2013 and 2014.

This is a levy on public servants. It is unrelated to the costs of the scheme and it is all the more difficult to take in the middle of a pay freeze of up to three years for civil servants, with further pay restraint to follow. Add to that the government's decision to devalue pensions in payment by switching the uprating index from the retail prices index to the lower consumer prices index and it is clear why many FDA members remain angry and resentful.

However, the government's final offer is the conclusion of almost two years of lobbying, submission of evidence, negotiation and industrial action – a first for the FDA – alongside many other public sector unions. In this time, progress has been made on some key issues, but, inevitably, we have not been able to move the government on others.

When the final offer was presented in March, the FDA found itself in a position where we recognised this was the best that could be achieved through negotiations. Understanding how difficult the decision would be for members, the FDA executive committee did not make a recommendation to either accept or reject the government's deal. The proposed new scheme remains a high-quality defined benefit scheme, but the changes will impact on members depending on variables such as age, when a member plans to retire and existing pension provision.

We were honest with members about their choice: accept the offer on the table, however reluctantly, or commit to sustained industrial action to move the government from its final and inevitably more entrenched position. That members voted to accept when faced with this choice should not be interpreted as a victory for the government.

Pensions are only one aspect of the total reward package, and the FDA has consistently maintained that pensions should not be considered in isolation. There is considerable evidence, including the government's own analysis, that the pay levels of those in the more senior roles of the civil service are substantially below those for comparable jobs in the wider public and private sectors, with the differential increasing the higher up the grading structure you go. The government has missed an opportunity to address this issue by rejecting our calls for a structured review as part of the pensions deal, and we are starting to see turnover rates in parts of the civil service of nearly a third, as committed, talented public servants opt for greater reward elsewhere.

There are few civil servants who are attracted to the role for high reward; most are committed to public service and the unique opportunities that come with the job. But when the disparity between the package available – pay and pension but also development, career progression and recognition – becomes too great, as it is now, then many will opt to go elsewhere and those who remain will do so with lingering resentment and frustration. This issue was recognised last week by Lord Browne, the government's own lead non-executive director in the civil service.

If the government wants high-quality public services delivered by high-quality public servants, then a fair package needs to be on offer. Ministers may now feel they can put public sector pension reform in the "out" tray, but for FDA members the demands for a "new deal" grow ever greater.